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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acgaacaaggccttagtcttttttatttgaacactagaccgcatctttttgtgtgtgtgtgattgtttatacttgcatcttacattctgaatctgactagGTGTGGCAACTGGAATGGGACATGGGCGGTATGACACTCGCATCAACCGGAGGAGATGGCATGGTTAAGCTATGGCAGGCTAATTTGGATGGAGTTTGGC

Basic information

species Zea mays
transcript GRMZM2G057853_T01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G057853_T01 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os01g43250.1 (Oryza sativa), 3'ss of exon 7
--------------------------------------------------------------------------acgaacaaggc--cttagtcttttttatttgaacactagaccgcatctttttgtgtgtgtgtgattgtttatact---tgcat-cttacattctgaatctgactagGTGTGGCAACTGGAATGGGACATGGGCGGTATGACACTCGCATCAACCGGAGGAGATGGCATGGTTAAGCTATGGCAGGCTAATTTGGATGGAGTTTGGC
                                                                              |  ||||  |||      ||  | |  |     |||   |   |  | ||||   | | | || |||| |      ||| |||   ||    | || |||||||   ||||||||||||||||||||||||||||||||||||||| |||||||| |||||||||||||||||||||||||||||  || ||||||||||||
gtacaataaacttgtcttgtctttgtgcagtagttattggctgtattacatgggctttctggagaatgtcttttgttcatgaggctccttgagaaattacagtatagttgaagaggactggtcctagtgtaatttttactgattattcggtacacatgcttgtttttcacaccttactagGTCCTGCAACTGGAATGGGACATGGGCGGTATGACACTCGCATCGACCGGAGGTGATGGCATGGTTAAGCTATGGCAGGCTAACCTGAATGGAGTTTGGC

upper sequence: GRMZM2G057853_T01 (Zea mays), 3'ss of exon 7
lower sequence: Vv02s0025g01250.t01 (Vitis vinifera), 3'ss of exon 7
acgaacaaggccttagtcttttttatttgaacactagaccgcatctttttgtgtg-tgtgtgattgtttatacttgcat---cttacattc-tgaatctgactagGTGTGGCAACTGGAATGGGACATGGGCGGTATGACACTCGCATCAACCGGAGGAGATGGCATGGTTAAGCTATGGCAGGCTAATTTGGATGGAGTTTGGC
    | |||  |||| ||||  |  ||| |  |    |     || | |  |||| ||| | | ||  |||  |   ||   | || |||| |   | ||| |||||||||||  |||||||||||||| |||| |||||  | ||| | || ||||||||||| ||||| | ||| |||||| |||| ||| |||| |||||||
----aaaagtacttattcttgatggttttagtaa-gcatgaactcatctgatgtgctgtattaatgaatatggtctgattgtcatatattcattgttgtgattagGTGTGGCAGATGGAATGGGACATGAGCGGAATGACCTTGGCAACTACTGGAGGAGATGGGATGGTAAGGCTGTGGCAGTCTAACTTGAATGGTGTTTGGC
















Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|148930898|gb|EC873352.2|EC873352
EST:     GCGGACCTTCGACGCAGAACGTTGCTTTACTTTATGGGCACGATGGCGAG                         GTGTGGCAACTGGAATGG
genomic: GCGGACCTTCGACGCAGAACGTTGCTTTACTTAATGGCCACGATGGCGAGgtacagctga ... atctgactagGTGTGGCAACTGGAATGG
EST: gi|50328004|gb|CO523130.1|CO523130
EST:     GCGGACCTTCGACGCAGAACGTTGCTTTACTTAATGGCCACGATGGCGAG                         GTGTGGCAACTGGAATGGGACATGGGCGGTATGACACTCGCATCAACCGGA
genomic: GCGGACCTTCGACGCAGAACGTTGCTTTACTTAATGGCCACGATGGCGAGgtacagctga ... atctgactagGTGTGGCAACTGGAATGGGACATGGGCGGTATGACACTCGCATCAACCGGA
EST: gi|149107563|gb|EE189446.2|EE189446
EST:     GCGGACCTTCGACGCAGAACGTTGCTTTACTTAATGGCCACGATGGCGAG                         GTGTGGCAACTGGAATGGGACATGGGCGGTATGACACTCGCATCAACCGGA
genomic: GCGGACCTTCGACGCAGAACGTTGCTTTACTTAATGGCCACGATGGCGAGgtacagctga ... atctgactagGTGTGGCAACTGGAATGGGACATGGGCGGTATGACACTCGCATCAACCGGA
EST: gi|71773952|gb|DR971840.1|DR971840
EST:     GCGGACCTTCGACGCAGAACGTTGCTTTACTTAATGGCCACGATGGCGAG                         GTGTGGCAACTGGAATGGGACATGGGCGGTATGACACTCGCATCAACCGGA
genomic: GCGGACCTTCGACGCAGAACGTTGCTTTACTTAATGGCCACGATGGCGAGgtacagctga ... atctgactagGTGTGGCAACTGGAATGGGACATGGGCGGTATGACACTCGCATCAACCGGA
EST: gi|148981980|gb|EE028040.2|EE028040
EST:     CGGGAC-TTCGACGCAAAACGTTGCTTTACTTAATGGCCACGATGGCGAG                         GTGTGGCAACTGGAATGG
genomic: CGG-ACCTTCGACGCAGAACGTTGCTTTACTTAATGGCCACGATGGCGAGgtacagctga ... atctgactagGTGTGGCAACTGGAATGG
EST: gi|211023881|gb|FL345725.1|FL345725
EST:     GCGGACCTTCGACGCAGAACGTTGCTTTACTTAATGGCCACGATGGCGAG                         GTGTGGCAACTGGAATGGGACATGGGCGGTATGACACTCGCATCAACCGGA
genomic: GCGGACCTTCGACGCAGAACGTTGCTTTACTTAATGGCCACGATGGCGAGgtacagctga ... atctgactagGTGTGGCAACTGGAATGGGACATGGGCGGTATGACACTCGCATCAACCGGA
EST: gi|84976699|gb|DW475121.1|DW475121
EST:     GTGGACCTTCGACGCAGAACGTTGCTTTACTTAATGGCCATGATGGCGAG                         GTGTGGCAACTGGAATGGGACATGGGC
genomic: GCGGACCTTCGACGCAGAACGTTGCTTTACTTAATGGCCACGATGGCGAGgtacagctga ... atctgactagGTGTGGCAACTGGAATGGGACATGGGC
EST: gi|71429467|gb|DR810517.1|DR810517
EST:     GCGGACCTTCGACGCAGAACGTTGCTTTACTTAATGGCCACGATGGCGAG                         GTGTGGCAACTGGAATGGGACATGGGCGGTATGACACTCGCATCAACCGGA
genomic: GCGGACCTTCGACGCAGAACGTTGCTTTACTTAATGGCCACGATGGCGAGgtacagctga ... atctgactagGTGTGGCAACTGGAATGGGACATGGGCGGTATGACACTCGCATCAACCGGA
EST: gi|148953594|gb|EC898948.2|EC898948
EST:     GCGGACCTTCGACGCAGAACGTTGCTTTACTTAATGGCCACGATGGCGAG                         GTGTGGCAACTGGAATGGGACATGGGCGGTATGACACTCGCATCAACCGGA
genomic: GCGGACCTTCGACGCAGAACGTTGCTTTACTTAATGGCCACGATGGCGAGgtacagctga ... atctgactagGTGTGGCAACTGGAATGGGACATGGGCGGTATGACACTCGCATCAACCGGA
EST: gi|60353460|gb|DN220433.1|DN220433
EST:     GCGGACCTTCGACGCAGAACGTTGCTTTACTTAATGGCCACGATGGCGAG                         GTGTGGCAACTGGAATGGGACATGGGCGGTATGACACTCGCATCAACCGGA
genomic: GCGGACCTTCGACGCAGAACGTTGCTTTACTTAATGGCCACGATGGCGAGgtacagctga ... atctgactagGTGTGGCAACTGGAATGGGACATGGGCGGTATGACACTCGCATCAACCGGA
EST: gi|76283890|gb|DV023458.1|DV023458
EST:     GCGGACCTTCGACGCAGAACGTTGCTTTACTTAATGGCCACGATGGCGAG                         GTGTGGCAACTGGAATGGGACATGGGCGGTATGACACTCGCATCAACCGGA
genomic: GCGGACCTTCGACGCAGAACGTTGCTTTACTTAATGGCCACGATGGCGAGgtacagctga ... atctgactagGTGTGGCAACTGGAATGGGACATGGGCGGTATGACACTCGCATCAACCGGA

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 101

CTGCAAAGGAATTGCAATCTGGCATATAGGTTTGAACGCTGATGCTGATGGCGGACCTTCGACGCAGAACGTTGCTTTACTTAATGGCCACGATGGCGAGgtacagctga ... atctgactagGTGTGGCAACTGGAATGGGACATGGGCGGTATGACACTCGCATCAACCGGAGGAGATGGCATGGTTAAGCTATGGCAGGCTAATTTGGATGGAGTTTGGC


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 70

CTGCAAAGGAATTGCAATCTGGCATATAGGTTTGAACGCTGATGCTGATGGCGGACCTTCGACGCAGAACGTTGCTTTACTTAATGGCCACGATGGCGAGgtacagctga ... atctgactagGTGTGGCAACTGGAATGGGACATGGGCGGTATGACACTCGCATCAACCGGAGGAGATGGCATGGTTAAGCTATGGCAGGCTAATTTGGATGGAGTTTGGC


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 92

CTGCAAAGGAATTGCAATCTGGCATATAGGTTTGAACGCTGATGCTGATGGCGGACCTTCGACGCAGAACGTTGCTTTACTTAATGGCCACGATGGCGAGgtacagctga ... atctgactagGTGTGGCAACTGGAATGGGACATGGGCGGTATGACACTCGCATCAACCGGAGGAGATGGCATGGTTAAGCTATGGCAGGCTAATTTGGATGGAGTTTGGC


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 51

CTGCAAAGGAATTGCAATCTGGCATATAGGTTTGAACGCTGATGCTGATGGCGGACCTTCGACGCAGAACGTTGCTTTACTTAATGGCCACGATGGCGAGgtacagctga ... atctgactagGTGTGGCAACTGGAATGGGACATGGGCGGTATGACACTCGCATCAACCGGAGGAGATGGCATGGTTAAGCTATGGCAGGCTAATTTGGATGGAGTTTGGC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttttgtgtgtgtgtgattgtttatacttgcatcttacattctgaatctgactagGTGTGGCAACTGGAATGGGACATGGGCGGTATGACACTCGCATCAACCGGAGGAGATGGCATGGTTAAGCTATGGCAGGCTAATTTGGATGGAGTTTGGC
                               atcttac  putative branch site (score: 51)
                attgtttata  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
acgaacaaggccttagtcttttttatttgaacactagaccgcatctttttgtgtgtgtgtgattgtttatacttgcatcttacattctgaatctgactagGTGTGGCAACTGGAATGGGACATGGGCGGTATGACACTCGCATCAACCGGAGGAGATGGCATGGTTAAGCTATGGCAGGCTAATTTGGATGGAGTTTGGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- gaacaag
- - - - - - - - - - - - - - -aacacta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgtgatt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tacttgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cattctg